As suggested by Larry Snyder in the comments to your question, you can reduce your problem to a standard traveling salesman problem by means of precomputing the distances. In particular, consider the complete graph with nodes given by $S$. Moreover, consider as distance between nodes $s_1$ and $s_2$ the shortest path between those nodes in your original graph $G$ (and a distance of $\infty$ if no path exists).
You are now left with a standard traveling salesman problem on which both types of formulations can be used. For some more information on what the best performing formulation would be, see the information in this question. In particular, note that the Dantzig-Fulkerson-Johnson (DFJ) is generally seen as the best performing formulation.
In case the paths between any two nodes in $S$ needs to be determined in the model (while the whole thing should still be a tour), you could adjust the DFJ formulation to account for only having to visit the nodes in $S$. In particular, replace the typical constraints
\begin{align}
& \sum_{j=1}^{n} x_{ij} = 1 && \forall i \in V,\\
& \sum_{i=1}^{n} x_{ij} = 1 && \forall j \in V,\\
\end{align}
by
\begin{align}
& \sum_{j=1}^{n} x_{ij} = 1 && \forall i \in S,\\
& \sum_{i=1}^{n} x_{ij} = 1 && \forall j \in S,\\
& \sum_{j=1}^{n} x_{ij} = \sum_{j=1}^{n} x_{ji} && \forall i \in V \setminus S.
\end{align}
Note that these constraints imply that there is again a collection of tours.
As for the regular TSP, it is needed to include subtour elimination constraints. In particular, we want to prevent that there are subtours that include only a subset of the nodes in $S$ (or subtours containing no nodes in $S$). We thus need to add a subtour elimination constraint for each $V' \subset V: S \nsubseteq V'$.